9-72900198-T-C

Variant names:

• chr9-72900198-T-C
• rs348483

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.108 in 152,150 control chromosomes in the GnomAD database, including 1,101 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (1101 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16467 AN: 152032 Hom.: 1101 Cov.: 32

Gnomad AFR AF: 0.0440

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.0799

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.0149

Gnomad SAS AF: 0.0578

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.111

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.108 AC: 16462 AN: 152150 Hom.: 1101 Cov.: 32 AF XY: 0.104 AC XY: 7721 AN XY: 74382

African (AFR) AF: 0.0441 AC: 1830 AN: 41536

American (AMR) AF: 0.0797 AC: 1218 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3460

East Asian (EAS) AF: 0.0147 AC: 76 AN: 5168

South Asian (SAS) AF: 0.0576 AC: 278 AN: 4824

European-Finnish (FIN) AF: 0.107 AC: 1132 AN: 10582

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10853 AN: 67982

Other (OTH) AF: 0.109 AC: 231 AN: 2112

Alfa AF: 0.146 Hom.: 2888

Bravo AF: 0.105

Asia WGS AF: 0.0510 AC: 175 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.55
PhyloP100		-0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs348483; hg19: chr9-75515114;